Daniel FischerBuffalo Center of Excellence in Bioinformatics, and Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, NY 14260, USACurr Opin Struct Biol 16:178-82. 2006

FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments

..Here we carry out a comprehensive, genome-wide study on the origins of ORFans to quantify the strength of current evidence supporting this hypothesis...

Servers for protein structure prediction

Daniel FischerBuffalo Center of Excellence in Bioinformatics, and Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, NY 14260, USACurr Opin Struct Biol 16:178-82. 2006

..Recent experiments suggest that servers will soon free humans from most of the burden of protein structure prediction...

FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments

..Recently, studies attempting to understand the origin and functions of bacterial ORFans have been reported. Here we present a first genome-wide identification and analysis of ORFans in the viral world, with focus on bacteriophages...

..Although this survey sheds some light on the ORFan mystery, further experimental studies are required to gain a better understanding of the role and origins of the tens of thousands of ORFans awaiting characterization...

..More importantly, LiveBench-8 identifies a handful of recently developed autonomous (nonmeta) servers that perform at the very top, suggesting that further progress in the individual methods has recently been obtained...

..In addition to the growing number of participants, the current experiment marks the introduction of new evaluation procedures, which are aimed to correlate better with functional characteristics of models...

..This result shows that significant progress has been achieved in automatic structure prediction and has important implications to the prospects of automated structure modeling in the context of structural genomics...

..We also describe the initiation of the two new, community-wide experiments, PDB-CAFASP and MR-CAFASP. These new experiments extend the scope of previous efforts and may have important implications for structural genomics...